CDSbank

CDSbank manages extraction, selection, renaming, and formatting of protein-coding DNA (CDS) sequences and their translated amino acid sequences to support comparative analyses of sequence, structure, function, and evolution.

Key Features:

• Integrated Sequence Storage: Stores protein-coding DNA (CDS) sequences and corresponding amino acid sequences for each protein annotated in GenBank.
• Rich Annotation Data: Retains GenBank feature annotations, flags for incomplete 5' and 3' ends, full taxonomic data, and a heuristic ranking of species scientific interest.
• Automated Dataset Preparation: Provides automated processes to prepare high-quality sequence datasets with configurable defaults and customization.
• Taxonomy-Aware Processing: Supports taxonomy-aware extraction and labeling of sequences for organism-specific selection and naming.
• Handling Incomplete Sequences: Identifies and flags incomplete 5' and 3' ends to account for sequence incompleteness in downstream analyses.
• Cross-Species Sequence Extraction: Extracts synonymous CDS or identical protein sequences across different species based on a single input protein sequence.
• Property File Creation: Generates labeled property files for annotating or relabeling phylogenetic trees.

Scientific Applications:

• Comparative Genomics: Assembling homologous CDS and protein sets across taxa for comparative analyses of sequence and function.
• Molecular Evolution: Selecting taxonomically informed sequence collections and completeness-filtered datasets for evolutionary inference.
• Functional Annotation: Supporting functional inference by providing CDS and protein sequences with GenBank feature annotations and completeness flags.
• Phylogenetic Annotation: Producing labeled property files to annotate or relabel phylogenetic trees for interpretation of evolutionary relationships.

Methodology:

Stores CDS and translated amino acid sequences for proteins annotated in GenBank, records GenBank feature annotations and flags for incomplete 5' and 3' ends, includes full taxonomic data and a heuristic species-interest ranking, performs taxonomy-aware extraction and labeling, extracts synonymous CDS or identical proteins across species from a single input sequence, generates labeled property files, and provides automated dataset preparation with configurable defaults.